SMTL ID : 3tnd.1

Crystal structure of Shigella flexneri VapBC toxin-antitoxin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-4-mer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: K.49 Chain B: N.69, E.71 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.69 Water bridges: B:D.65, A:K.49 Salt bridges: A:K.49 SO4.3: 4 residues within 4Å: Chain B: R.21, P.23, K.24 Chain D: S.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.24 Salt bridges: B:R.21 SO4.5: 4 residues within 4Å: Chain B: S.17 Chain D: R.21, P.23, K.24 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.24, B:S.17, B:S.17 Salt bridges: D:R.21 SO4.6: 1 residues within 4Å: Chain D: R.21 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.21 SO4.7: 3 residues within 4Å: Chain E: R.55 Chain F: S.63, T.64 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Salt bridges: E:R.55 Hydrogen bonds: F:T.64 SO4.8: 3 residues within 4Å: Chain F: R.21, P.23, K.24 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.24 Salt bridges: F:R.21, F:K.24 SO4.9: 3 residues within 4Å: Chain C: L.126 Chain G: G.125, L.126 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:G.125, G:L.126, C:G.125, C:L.126 Water bridges: G:E.121, G:V.123 SO4.10: 4 residues within 4Å: Chain F: R.34 Chain H: T.9, T.10, R.21 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain H Salt bridges: F:R.34, H:R.21 Hydrogen bonds: H:T.10, H:T.10, H:T.10 SO4.11: 4 residues within 4Å: Chain F: S.17 Chain H: R.21, P.23, K.24 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:S.17, H:K.24 Salt bridges: H:R.21 SO4.12: 2 residues within 4Å: Chain G: K.49 Chain H: N.69 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:N.69 Water bridges: H:D.65, G:K.49 Salt bridges: G:K.49 SO4.13: 3 residues within 4Å: Chain G: R.55 Chain H: H.60, S.61 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Water bridges: G:R.55, G:R.55 Salt bridges: G:R.55, H:H.60 Hydrogen bonds: H:S.61

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain B: R.70, Q.72 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.70, B:Q.72 Water bridges: A:N.9, A:N.9, A:D.98 NA.4: 1 residues within 4Å: Chain D: Q.72 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.72 Water bridges: D:R.70, D:R.70, D:Q.72, D:Q.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dienemann, C. et al., Crystal Structure of the VapBC Toxin-Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly. J.Mol.Biol. (2011)

Release Date

2011-11-02

Peptides

tRNA(fMet)-specific endonuclease VapC: ACEG
Antitoxin VapB: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

tRNA(fMet)-specific endonuclease VapC

Antitoxin VapB